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Joint Genotyping

I ran GATKHaplotypeCaller without GVCF mode. I have got the correct output VCF file. I want to do the joint Genotyping for BSA QTLSeqr analysis. The GATK GenoType is only for gVCF. I cannot run this mode, it takes too much time, even if run the aligner file in intervals. My question, how can I use the joint GenoTyping on the VCF file.
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